Infant formulas (IFs), the only adequate substitute to breastmilk, are complex matrices that require numerous ingredients and processing steps. The objective was to understand how protein structure within IFs modulates their digestive kinetics. Four IFs (A/B/C/D), containing whey protein (WP) ingredients with different denaturation and glycation levels (A/B/C) and caseins with different structures (C/D), were subjected to infant in vitro dynamic digestion (DIDGI®). Digesta were regularly sampled to follow structural changes (A4F, microscopy), proteolysis (OPA, LC-MS-MS) and lipolysis (GC-MS). Data were analysed using repeated measures ANOVA. Before digestion, lipoprotein structures were different among IFs. IF-A, characterized by higher glycated and denatured WP rates, tended to be more digested at 180min of intestinal phase than IF-C/D (degree of proteolysis +16% and lipolysis +5.2%). Peptides (protein-origin independent) appeared sooner into the gastric phase for IF-D (at 80 min vs. 180 min for IF-A/B), suggesting that the initial bigger lipoprotein structures in the matrix were less dense and more accessible to pepsin. Different bioactive peptides kinetics were also observed among IFs during digestion. Overall, it highlights the importance of the structure of protein ingredients (WPs and caseins) selected for IFs. Further investigation will be conducted in vivo (mini-piglets) to complete these data.